Mercurial > repos > rmarenco > hubarchivecreator

comparison util/subtools.py @ 26:df42241d3731 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents 99dad5f9444c
children 7e8a8b732db3
comparison
equal deleted inserted replaced
25:99dad5f9444c 26:df42241d3731
180 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name] 180 array_call = ['sort', '-k2rn', two_bit_info_file_name, '-o', chrom_sizes_file_name]
181 p = _handleExceptionAndCheckCall(array_call) 181 p = _handleExceptionAndCheckCall(array_call)
182 return p 182 return p
183 183
184 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name, 184 def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,
185 typeOption=None, autoSql=None, tab=False): 185 typeOption=None, autoSql=None, tab=False, extraIndex=None):
186 """ 186 """
187 Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name 187 Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name
188 :param sorted_bed_file_name: 188 :param sorted_bed_file_name:
189 :param chrom_sizes_file_name: 189 :param chrom_sizes_file_name:
190 :param big_bed_file_name: 190 :param big_bed_file_name:
207 if autoSql: 207 if autoSql:
208 autoSql = ''.join(['-as=', autoSql]) 208 autoSql = ''.join(['-as=', autoSql])
209 array_call.append(autoSql) 209 array_call.append(autoSql)
210 if tab: 210 if tab:
211 array_call.append('-tab') 211 array_call.append('-tab')
212 if extraIndex:
213 index = ''.join(['-extraIndex=', extraIndex])
214 array_call.append(index)
212 215
213 p = _handleExceptionAndCheckCall(array_call) 216 p = _handleExceptionAndCheckCall(array_call)
214 return p 217 return p
215 218
216 def sortBam(input_bam_file_name, output_sorted_bam_name): 219 def sortBam(input_bam_file_name, output_sorted_bam_name):